Parallel transformers are used in substations to enhance reliability and power capacity. The substation operators may decide to close or open the coupling switches in the high/low voltage side of the transformers to make them work parallel with the isolated state. This may change the substation topology and the short circuit levels of its nodes. This can affect greatly the switching transients, especially for capacitor banks in or out. So, it may considerably increase the capacitor inrush currents. This may lead to capacitor bank’s overcurrent relay malfunction. In this paper, an analytical approach has been first developed to calculate the effect of the load harmonics on the capacitor bank inrush current. Then this method has been generalized to the case of having two power transformers in parallel in the substation. A 63/20 kV sub-transmission substation in Bakhtar Regional Power Company, including nonlinear loads (arcfurnaces), has been used as a case study to evaluate the method, and EMTP-RV software has been used to validate the results. The results show that a high nonlinear load may considerably increase the capacitor inrush current peak value and lead to overcurrent relay operation.